Re: [ccp4bb] Ramachandran plot, in a text list

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Subject: Re: Ramachandran plot, in a text list
From: Eleanor Dodson ccp4 {- at -} YSBL {- dot -} YORK {- dot -} AC {- dot -} UK
Date: 2009-01-15

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Subject: Re: Ramachandran plot, in a text list
From: MATSUURA Takanori t-matsuu {- at -} PROTEIN {- dot -} OSAKA-U {- dot -} AC {- dot -} JP
Date: 2009-01-15

Subject: Re: Ramachandran plot, in a text list
From: Martyn Winn martyn {- dot -} winn {- at -} STFC {- dot -} AC {- dot -} UK
Date: 2009-01-15

However, procheck ramachandran is deprecated these days as it is based
on older data than say molprobity. Obviously that won't matter just for
a list of phi/psi angles, but might affect selections e.g. what it
thinks are in a helix (cf Eleanor's message)

m

On Wed, 2009-01-14 at 14:39 -0500, Edward A. Berry wrote:
> John Pak wrote:
> > Hi, sorry if this was posted earlier. How can I calculate a
> > Ramachandran plot, but output the information to a text file list?
> > i.e. something like Ala51, phi=X, psi=Y.
> >
> > I can't seem to find this information in the ccp4 SFCheck/Procheck log
> > file.
> >
>
> And lets not forget procheck, since its included with ccp4 and you
> probably already have it. After you run procheck on your protein
> (procheck pdbname.pdb 1.8), there is a text file pdbname.rin
> which lists phi, psi, omega and sidechain dihedrals for each residue:
>
>
> phi psi omega chi1 chi2 chi3 chi4
> 14ASN A 15 E -89.06 141.45-179.73 -63.59 -55.39 999.90 999.90 -2.14 0.00 34.00 89.18 88.838 88.830 8 45 1.980 0.762
> 15VAL A 16 E-139.67 138.33 177.89-170.03 999.90 999.90 999.90 0.00 0.00 36.23 87.91 86.643 87.253 8 50 0.147 0.499
> 16THR A 17 E-144.59 139.86-179.12 51.94 999.90 999.90 999.90 -2.64 0.00 34.56 84.27 86.238 85.020 8 40 0.421 0.536
>
> You also have a .ps file pdbname_01.ps with the graphical ramachandran
> which you can view with gv or gs, or convert to pdf with ps2pdf
>
> DSSP also list phi-psi angles, in two columns far to the right.
>
> Ed
--
***********************************************************************
* *
* Dr. Martyn Winn *
* *
* STFC Daresbury Laboratory, Daresbury, Warrington, WA4 4AD, U.K. *
* Tel: +44 1925 603455 E-mail: martyn.winn@stfc.ac.uk *
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CCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999

Previous message:
Subject: Re: Ramachandran plot, in a text list
From: Eleanor Dodson ccp4 {- at -} YSBL {- dot -} YORK {- dot -} AC {- dot -} UK
Date: 2009-01-15

Next message:
Subject: Re: Ramachandran plot, in a text list
From: MATSUURA Takanori t-matsuu {- at -} PROTEIN {- dot -} OSAKA-U {- dot -} AC {- dot -} JP
Date: 2009-01-15